If you're stealing the enemy's flag and it does the animation, while you mass click your weapon in the inventory, the flag will appear in your inventory. You're character isn't holding the flag but the weapon you mass clicked. You can un-equip and equip weapons when the flag is still showing in the inventory. It will also show that you're holding the flag.

My ancient staff disappeared when I went to put the enemy flag back to our base. But the enemy's flag was still in my inventory. When the game ended, my ancient staff didn't appear in my inventory but the enemy's flag was still there but i couldn't equip it. After re-logging, the flag disappeared.

Sorry I didn't take a screenshot before I posted this.